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- PDB-1yu1: Major Tropism Determinant P3c Variant -

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Basic information

Entry
Database: PDB / ID: 1yu1
TitleMajor Tropism Determinant P3c Variant
ComponentsMajor Tropism Determinant (Mtd-P3c)
KeywordsVIRAL PROTEIN / C-type Lectin / Beta Sandwich / Beta Prism / variability / diversity-generating retroelement
Function / homology
Function and homology information


viral tropism switching / virus tail, fiber / adhesion receptor-mediated virion attachment to host cell / symbiont entry into host cell
Similarity search - Function
Seminal Fluid Protein PDC-109 (Domain B) - #30 / Tail fiber receptor-binding protein / Tail fiber receptor-binding protein / Major tropism determinant, N-terminal domain / Major tropism determinant N-terminal domain / paralog of FGE (formylglycine-generating enzyme) / paralog of FGE (formylglycine-generating enzyme) / Sulfatase-modifying factor enzyme superfamily / Seminal Fluid Protein PDC-109 (Domain B) / C-type lectin fold ...Seminal Fluid Protein PDC-109 (Domain B) - #30 / Tail fiber receptor-binding protein / Tail fiber receptor-binding protein / Major tropism determinant, N-terminal domain / Major tropism determinant N-terminal domain / paralog of FGE (formylglycine-generating enzyme) / paralog of FGE (formylglycine-generating enzyme) / Sulfatase-modifying factor enzyme superfamily / Seminal Fluid Protein PDC-109 (Domain B) / C-type lectin fold / Trefoil / Ribbon / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
METHYL MERCURY ION / Tail fiber receptor-binding protein
Similarity search - Component
Biological speciesBordetella phage BPP-1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsMcMahon, S.A. / Miller, J.L. / Lawton, J.A. / Ghosh, P.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2005
Title: The C-type lectin fold as an evolutionary solution for massive sequence variation
Authors: McMahon, S.A. / Miller, J.L. / Lawton, J.A. / Kerkow, D.E. / Hodes, A. / Marti-Renom, M.A. / Doulatov, S. / Narayanan, E. / Sali, A. / Miller, J.F. / Ghosh, P.
History
DepositionFeb 11, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2005Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 29, 2023Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_name
Remark 999SEQUENCE The author states there is an error in the database sequence.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major Tropism Determinant (Mtd-P3c)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9664
Polymers39,5101
Non-polymers4563
Water6,648369
1
A: Major Tropism Determinant (Mtd-P3c)
hetero molecules

A: Major Tropism Determinant (Mtd-P3c)
hetero molecules

A: Major Tropism Determinant (Mtd-P3c)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,89812
Polymers118,5313
Non-polymers1,3679
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area14250 Å2
ΔGint-92 kcal/mol
Surface area35050 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)66.545, 66.545, 334.953
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-383-

MG

21A-407-

HOH

31A-419-

HOH

41A-640-

HOH

DetailsThe biological assembly is a trimer generated from: -y, x-y, z and -x+y, -x, z

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Components

#1: Protein Major Tropism Determinant (Mtd-P3c)


Mass: 39510.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella phage BPP-1 (virus) / Plasmid: pGEX / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q775D6
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-MMC / METHYL MERCURY ION / Methylmercury


Mass: 215.625 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH3Hg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 369 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.5
Details: Lithium Sulfate, Tris, Sodium Chloride, pH 8.5, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.2309 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2309 Å / Relative weight: 1
ReflectionResolution: 2.07→50 Å / Num. all: 26802 / Num. obs: 26802 / % possible obs: 95.14 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.07→2.14 Å / % possible all: 94.2

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1YU0

1yu0


Resolution: 2.07→28.99 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.923 / SU B: 3.825 / SU ML: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.192 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2209 1340 5 %RANDOM
Rwork0.18234 ---
all0.18425 26802 --
obs0.18425 26802 95.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.951 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.07→28.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2753 0 5 369 3127
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0212823
X-RAY DIFFRACTIONr_bond_other_d0.0020.022424
X-RAY DIFFRACTIONr_angle_refined_deg1.0261.9023848
X-RAY DIFFRACTIONr_angle_other_deg0.76535609
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2835375
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0630.2426
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023290
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02617
X-RAY DIFFRACTIONr_nbd_refined0.2110.2556
X-RAY DIFFRACTIONr_nbd_other0.2340.22876
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0810.21547
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2244
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0880.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1230.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2610.2119
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.230
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.53921843
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.93432918
X-RAY DIFFRACTIONr_scbond_it0.5962980
X-RAY DIFFRACTIONr_scangle_it0.9543930
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.069→2.123 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.283 105
Rwork0.233 1775

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